This web page was produced as an assignment for an
undergraduate course at Davidson College.
MRPL28 Gene in Saccharomyces cerevisiae

Introduction

The MRPL28 gene in Saccharomyces cerevisiae
encodes for a protein that is found on the large ribosomal subunit on
the mitochondrial ribosome. Ribosomes are involved in the synthesis
of proteins in cells, and can occur in three main subcellular locations -
the cytosol, the endoplasmic reticulum, and the mitochondria. The function
is basically the same in all three places. The ribosome binds RNA, then codon
by codon, synthesizes an amino acid chain from the RNA code. Because
the ability to synthesize proteins is vital for the survival of any organism,
it is important to know the function, structure, variations, and problems
of the proteins that make up the ribosomes. Thus, MRPL28 is a crucial
gene to study.

Nucleotide
Information

The MRPL28 gene is
found on chromosome 4 in Saccharomyces cerevisiae. It
is a gene with a length of 444 base pairs, and codes for a protein (YmL28)
found in the large ribosomal subunit in this yeast. The protein
is involved in the synthesis of proteins. The location of the gene on
chromosome 4 is shown in this map, obtained from the
Saccharomyces Genome Database
:
(permission to use
image pending from
Saccharomyces Genome Database)

The nucleotide sequence for the MRPL28 gene was compared
with a BLAST search at the National
Center for Biotechnology Information
webpage, and it was found that there are several very similar nucleotide
sequences in different organisms. However, the only sequences that
matched with E-values of less than 1.0 were from Saccharomyces cerevisiae
. This relatively low amount of similarity between species shows a remarkably
low conservation for this protein in the mitochondrial ribosomes. In
fact, the most closely-related BLAST sequence is from the apolipoprotein-L
in Homo sapiens.

Protein Information

The
MRPL28 gene in Saccharomyces
cerevisiae
codes for the YmL28 protein, found in the large ribosomal subunit in the
ribosome of the mitochondria. The protein has a length of 147 amino
acids and a molecular weight of 17342 Da (
SwissProt
). The protein assists the large ribosomal subunit in translation
of RNA into proteins. This protein has not been crystallized yet,
and thus there is not a chime file showing the 3D structure of the protein.
When a BLAST search was performed, it was found that the most similar
protein is the RGS4 protein from Rattus norvegicus which "regulates
G protein signaling in the C. elegans nervous system and shares a conserved
domain with many mammalian proteins" (
Koelle, et al, 1996
). An attempt in
Swiss-Model
to determine similar 3D structures showed that there were no documented
proteins with a 3D stucture similar to MRPL28 with an E-value of <0.0001.
A
PREDATOR
search reveals that the protein is made up of 47.62% each of alpha-helices
and random coils, and 4.76% extended strand (
PREDATOR Search
). A hydropathy plot was then conducted, and it was found that the
protein is largely hydrophilic, with a small hydrophobic region around amino
acid numbers 15 through 23 and again from around amino acid numbers 35 through
50. The amino acid sequence for the MRPL28 protein is included below:

This gene was tested by Winzeler, et al for viability
when the ORF was deleted (
read the abstract
), and it was shown that the yeast was viable with the deletion of the
MRPL28 ORF (Winzeler, et al, 1999). This could mean one of two things:
either there is another gene which codes for a different protein
which in turn synthesizes the same proteins in the mitochondria, or that
the proteins produced in the mitochondria by the MRPL28 protein are not
necessary, and can be replaced by other proteins made from other ribosomal
proteins. However, as the effects of variation in this gene are unknown
at this time.

Conclusions

The study of the effects of changes in ribosomal
proteins is a very important one, as ribosomal proteins are extremely far
"upstream" in cellular pathways. It has been discovered in S. cerevisiae
that "only a minority of the MRPs [Mitochondrial Ribosomal Proteins] that
have been characterized show significant sequence similarities to known ribosomal
proteins from other sources" (
Graack HR, et al, 1998
).